SNP芯片评估柯尔克孜羊群体遗传多样性和遗传结构

doi:10.11843/j.issn.0366-6964.2023.02.015

Abstract

Abstract: The aim of this study was to investigate the genetic diversity and genetic structure of Kirgiz sheep, and effectively protect and utilize its genetic resources.Sheep SNP 50K v3 chip was used to detect the single nucleotide polymorphism (SNP) of 61 Kirgiz sheep (31 rams and 30 ewes). Plink software (V1.90) was used to conduct the quality control of SNP genotyping results, and calculate the population effective content, the polymorphic marker proportion, observed heterozygosity, expected heterozygosity, polymorphic information content, effective number of alleles, minor allele frequency to analyze the genetic diversity of the Kirgiz sheep; Using Plink to calculate the runs of homozygosity (ROH) and obtain the inbreeding coefficient F_ROH based on ROH; The state homologous distance matrix (identical by state, IBS) was established, and G matrix were constructed by Gmatrix software, the genetic distance and genetic relationship of Kirgiz sheep were explored. Mega X software was used to construct evolutionary tree and analyze the family structure of Kirgiz rams. The results showed that a total of 64 734 SNPs were obtained from 61 Kirgiz sheep, and the number of SNPs passing quality control was 56 763; The average polymorphism information content was 0.273±0.112, the average observed heterozygosity and the average expected heterozygosity were 0.368±0.140 and 0.368±0.130, respectively, and the average minor allele frequency was 0.263±0.147. The average IBS genetic distance of Kirgiz sheep was 0.294. The results of G matrix and IBS distance matrix showed that the genetic relationship between individuals of Kirgiz sheep was farther. A total of 200 ROHs were detected in 61 Kirgiz sheep, 67.5% of which were within 1-5 Mb in length, and the ROH length of 56 Kirgiz sheep was 0-50 Mb. The average inbreeding coefficient based on ROH was 0.008 19±0.018 8, of which the average inbreeding coefficient of rams was 0.004 65±0.008, indicating that the average inbreeding coefficient degree of Kirgiz sheep population was low. The results of phylogenetic tree showed that there were 25 families in Kirgiz sheep population, and most families have too few rams. To sum up, the Kirgiz sheep population has rich genetic diversity and low inbreeding degree in these population, but the number of male sheep in each family is small, so it is necessary to increase the breeding of offspring and prevent the loss of blood to maintain the genetic diversity of Kirgiz sheep.

Key words: Kirgiz sheep, SNPs chip, genetic diversity, genetic structure

CLC Number:

S826.2

LI Yinxia, YA Shengjiang·Nasier, SAI Like·Duman, QIAN Yong, CAO Shaoxian, WANG Weilie, MENG Chunhua, ZHANG Jun, ZHANG Jianli. Evaluation of Genetic Diversity and Genetic Structure in Kirgiz Sheep Population Based on SNPs Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 572-583.

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Evaluation of Genetic Diversity and Genetic Structure in Kirgiz Sheep Population Based on SNPs Chip

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